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Identification and Characterization of Novel Human Endogenous Retrovirus Families by Phylogenetic Screening of the Human Genome Mapping Project Database
Open accessAbstract
Human endogenous retroviruses (HERVs) were first identified almost 20 years ago, and since then numerous families have been described. It has, however, been difficult to obtain a good estimate of both the total number of independently derived families and their relationship to each other as well as to other members of the family Retroviridae . In this study, I used sequence data derived from over 150 novel HERVs, obtained from the Human Genome Mapping Project database, and a variety of recently identified nonhuman retroviruses to classify the HERVs into 22 independently acquired families. Of these, 17 families were loosely assigned to the class I HERVs, 3 to the class II HERVs and 2 to the class III HERVs. Many of these families have been identified previously, but six are described here for the first time and another four, for which only partial sequence information was previously available, were further characterized. Members of each of the 10 families are defective, and calculation of their integration dates suggested that most of them are likely to have been present within the human lineage since it diverged from the Old World monkeys more than 25 million years ago.
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“In the case of endogenous retroviruses (embedded in the genome of their host), dates of origin can be estimated without a calibration date by comparing the two long terminal repeats (LTRs) that flank the viral genome - a method that has helped uncover the history of viral DNA in the human genome 60,61 .”
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Metadata
- Authors
- Tristem, M.
- Affiliations
- Imperial College London (GB)
- Corresponding author
- Tristem, Michael
- ORCID
- Tristem, Michael
- Venue
- Journal of Virology
- Publisher
- American Society for Microbiology
- Published
- 2000-04-15
- Volume
- 74
- Issue
- 8
- Pages
- 3715-3730
- ISSN
- 0022-538X (ISSN-L)
- 1098-5514
- PMC
- PMC111881
- OpenAlex
- W2082918825
- Cited by
- 330
- References
- 64
- Citations by year
- 2026: 1 · 2025: 6 · 2024: 9 · 2023: 7 · 2022: 5 · 2021: 12 · 2020: 6 · 2019: 11 · 2018: 8 · 2017: 13 · 2016: 11 · 2015: 15 · 2014: 12 · 2013: 18 · 2012: 16
- FWCI
- 34.65
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Virology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Royal Society
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Health Sciences › Medicine › Infectious Diseases › Infectious Diseases and Mycology
- Keywords
- human endogenous retroviruses, phylogenetic analysis, human evolution, Old World monkeys, retroviral evolution
- MeSH terms
- Amino Acid Sequence, Animals, Base Sequence, Chromosome Mapping, Humans, Molecular Sequence Data, Terminology as Topic, Phylogeny, Human Genome Project, Databases, Factual, Sequence Alignment, Sequence Analysis, DNA, Endogenous Retroviruses
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